Well, Godot doesn't install. It's just the executable file. So if the editor could not create those folders, it probably means the permissions are still wrong and some stuff might break. To change permissions you can use the command line console (in Linux, should be installed already) with the command "chmod" applied to the Godot executable. I think 755 should work, but read up on chmod so you understand what you are doing (and what to do if you mess something up).
